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- PDB-7bxb: Crystal structure of Ca_00311 -

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基本情報

登録情報
データベース: PDB / ID: 7bxb
タイトルCrystal structure of Ca_00311
要素GDSL-like Lipase/Acylhydrolase
キーワードHYDROLASE
機能・相同性SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / carboxylic ester hydrolase activity / PHOSPHATE ION / GDSL-like Lipase/Acylhydrolase
機能・相同性情報
生物種Collinsella aerofaciens (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.72 Å
データ登録者Fan, C.P.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China (NSFC)31570762 中国
引用ジャーナル: To Be Published
タイトル: crystal structure of Ca_00311
著者: Fan, C.P.
履歴
登録2020年4月18日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年4月21日Provider: repository / タイプ: Initial release
改定 1.12023年11月29日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: GDSL-like Lipase/Acylhydrolase
B: GDSL-like Lipase/Acylhydrolase
C: GDSL-like Lipase/Acylhydrolase
D: GDSL-like Lipase/Acylhydrolase
E: GDSL-like Lipase/Acylhydrolase
F: GDSL-like Lipase/Acylhydrolase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)147,40821
ポリマ－145,9846
非ポリマー1,42515
水25,6171422
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18600 Å2
ΔGint-192 kcal/mol
Surface area43970 Å2
手法PISA
単位格子
Length a, b, c (Å)112.929, 112.929, 305.943
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEU(chain 'A' and (resid 0 through 43 or resid 45...AA0 - 421 - 43
12GLYGLYPHEPHE(chain 'A' and (resid 0 through 43 or resid 45...AA45 - 15446 - 155
13HISHISVALVAL(chain 'A' and (resid 0 through 43 or resid 45...AA157 - 172158 - 173
14PHEPHEMETMET(chain 'A' and (resid 0 through 43 or resid 45...AA176 - 198177 - 199
15SERSERLEULEU(chain 'A' and (resid 0 through 43 or resid 45...AA201 - 217202 - 218
26ALAALALEULEU(chain 'B' and (resid 0 through 43 or resid 45...BB0 - 421 - 43
27GLYGLYPHEPHE(chain 'B' and (resid 0 through 43 or resid 45...BB45 - 15446 - 155
28HISHISVALVAL(chain 'B' and (resid 0 through 43 or resid 45...BB157 - 172158 - 173
29PHEPHEMETMET(chain 'B' and (resid 0 through 43 or resid 45...BB176 - 198177 - 199
210SERSERLEULEU(chain 'B' and (resid 0 through 43 or resid 45...BB201 - 217202 - 218
311ALAALALEULEU(chain 'C' and (resid 0 through 43 or resid 45...CC0 - 421 - 43
312GLYGLYPHEPHE(chain 'C' and (resid 0 through 43 or resid 45...CC45 - 15446 - 155
313HISHISVALVAL(chain 'C' and (resid 0 through 43 or resid 45...CC157 - 172158 - 173
314PHEPHEMETMET(chain 'C' and (resid 0 through 43 or resid 45...CC176 - 198177 - 199
315SERSERLEULEU(chain 'C' and (resid 0 through 43 or resid 45...CC201 - 217202 - 218
416ALAALALEULEU(chain 'D' and (resid 0 through 43 or resid 45...DD0 - 421 - 43
417GLYGLYPHEPHE(chain 'D' and (resid 0 through 43 or resid 45...DD45 - 15446 - 155
418HISHISVALVAL(chain 'D' and (resid 0 through 43 or resid 45...DD157 - 172158 - 173
419PHEPHEMETMET(chain 'D' and (resid 0 through 43 or resid 45...DD176 - 198177 - 199
420SERSERLEULEU(chain 'D' and (resid 0 through 43 or resid 45...DD201 - 217202 - 218
521ALAALALEULEU(chain 'E' and (resid 0 through 43 or resid 45...EE0 - 421 - 43
522GLYGLYPHEPHE(chain 'E' and (resid 0 through 43 or resid 45...EE45 - 15446 - 155
523HISHISVALVAL(chain 'E' and (resid 0 through 43 or resid 45...EE157 - 172158 - 173
524PHEPHEMETMET(chain 'E' and (resid 0 through 43 or resid 45...EE176 - 198177 - 199
525SERSERLEULEU(chain 'E' and (resid 0 through 43 or resid 45...EE201 - 217202 - 218
626ALAALALEULEU(chain 'F' and (resid 0 through 43 or resid 45...FF0 - 421 - 43
627GLYGLYPHEPHE(chain 'F' and (resid 0 through 43 or resid 45...FF45 - 15446 - 155
628HISHISVALVAL(chain 'F' and (resid 0 through 43 or resid 45...FF157 - 172158 - 173
629PHEPHEMETMET(chain 'F' and (resid 0 through 43 or resid 45...FF176 - 198177 - 199
630SERSERLEULEU(chain 'F' and (resid 0 through 43 or resid 45...FF201 - 217202 - 218

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要素

#1: タンパク質
GDSL-like Lipase/Acylhydrolase / Ca_00311


分子量: 24330.625 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Collinsella aerofaciens (バクテリア)
遺伝子: NCTC11838_00845 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A381K2L8
#2: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 15 / 由来タイプ: 合成 / 式: PO4
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1422 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.34 Å3/Da / 溶媒含有率: 63.23 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 0.1M pH7.50, 0.8 sodium phosphate monobasic, 0.8M potassium phosphate monobasic

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL19U1 / 波長: 0.9793 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2020年1月1日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9793 Å / 相対比: 1
反射解像度: 1.72→48.57 Å / Num. obs: 211217 / % possible obs: 100 % / 冗長度: 23.5 % / Biso Wilson estimate: 19.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.029 / Rrim(I) all: 0.142 / Rsym value: 0.138 / Net I/σ(I): 20.3
反射 シェル解像度: 1.72→1.74 Å / Rmerge(I) obs: 1.383 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 10262 / CC1/2: 0.565 / Rpim(I) all: 0.421 / Rrim(I) all: 1.449 / Rsym value: 1.383

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
XDSデータ削減
Aimlessデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4XT1

4xt1


解像度: 1.72→48.57 Å / SU ML: 0.1744 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 18.2012
Rfactor反射数%反射
Rfree0.1938 1999 5 %
Rwork0.1608 --
obs0.1611 210916 99.85 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 23.22 Å2
精密化ステップサイクル: LAST / 解像度: 1.72→48.57 Å
タンパク質核酸リガンド溶媒全体
原子数10153 0 75 1422 11650
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.014210447
X-RAY DIFFRACTIONf_angle_d1.285314192
X-RAY DIFFRACTIONf_chiral_restr0.0861530
X-RAY DIFFRACTIONf_plane_restr0.00871873
X-RAY DIFFRACTIONf_dihedral_angle_d4.08746173
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.760.33011390.273514619X-RAY DIFFRACTION99.14
1.76-1.810.2261420.223614748X-RAY DIFFRACTION99.97
1.81-1.860.24321410.198514788X-RAY DIFFRACTION99.99
1.86-1.920.2111420.188814780X-RAY DIFFRACTION99.96
1.92-1.990.19091410.179814779X-RAY DIFFRACTION99.95
1.99-2.070.18081420.162914821X-RAY DIFFRACTION99.92
2.07-2.160.21021420.162214804X-RAY DIFFRACTION99.92
2.16-2.270.18811420.157814841X-RAY DIFFRACTION99.82
2.27-2.420.20311410.1614868X-RAY DIFFRACTION99.79
2.42-2.60.18981430.160814891X-RAY DIFFRACTION99.8
2.6-2.870.19081440.164314960X-RAY DIFFRACTION99.88
2.87-3.280.21141430.1615061X-RAY DIFFRACTION99.89
3.28-4.130.19341460.135915179X-RAY DIFFRACTION99.89
4.13-48.570.14991510.144215778X-RAY DIFFRACTION99.94
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.169801686481.041924860080.2987308612534.457225736980.3120507892611.85951197226-0.0164766092285-0.006577035093240.07047992607490.05177124031530.0876919852997-0.0716743190792-0.01945488650360.215760351432-0.06380528226120.1518652198680.0362657440464-0.007970960150210.188292499865-0.02344991399420.0992678949655-42.9514732803-0.193308011274-11.1565663553
25.09666821687-0.07501055826070.0004372322589044.244624724960.6059119452456.67669894829-0.024157080924-0.2309771631530.263620401-0.09218206751550.0366627603343-0.4206504650540.02795625516410.7816426136310.01469974353350.1315936839910.0466319189765-0.0243512201880.319311023232-0.03121211590380.208714914084-34.07141866472.63185496807-9.50261280339
32.010761034561.32567406018-0.3275164550795.37877715299-1.991967463776.440995401870.0129789317782-0.148984551534-0.1438808768450.2992022974870.0383832139133-0.1740716909660.3235704035270.455393620987-0.05679623515240.1807912302310.0791546684823-0.02123409734290.203899683731-0.02177600959420.149928915701-43.7809724102-9.30546187093-5.10570554518
40.5738145236520.0380732928278-0.1298127462191.93730081659-0.1799695146530.68706472391-0.00650680906255-0.02082700116770.01326952117120.02152083461020.00798255513736-0.02666224552860.01669706030650.0211091095725-0.003472206021580.1401461761720.00146061083024-0.01098872016330.155326704111-0.008584950392240.138107998877-51.54127761961.64541220946-20.6104961568
50.869014894322-1.57116356102-0.2330858246798.923711323381.274510295291.06879663883-0.0165925668748-0.00547949239666-0.1631810601360.21029369983-0.03682511473210.3770891016280.129554256437-0.04965356726830.05234018953240.1478597862450.009073470942920.004049259515880.173805060990.003219221331760.168830069912-61.3078568906-6.44705260506-17.136627059
60.9713588743581.09286205865-0.3857772079252.14872415766-0.596496642741.00051459256-0.00085002177336-0.1303080136380.08530064058920.122362782638-0.0208915499635-0.0729350867363-0.1588006713630.09453195735560.01544510700660.1692705161030.00878833205144-0.009707573024980.189894030947-0.03505224879220.158265340875-50.378225920413.411325904-10.9129247607
74.673220332293.61387443021-0.8030719407312.81752143108-0.5172296382092.694170999370.0857626253515-0.2072994299340.2939960310030.2098986976520.02531440634470.41363621219-0.154645192961-0.279319273981-0.1145835177010.1504026304420.06500401517590.0111223169320.214342368546-0.01033556513310.183590620506-61.94291290979.78078154477-9.29139995899
82.591328843131.18411928747-1.248600494132.24140514586-1.084646651111.49614261451-0.0189920405007-0.1428072170850.09474951829250.2688700423940.0527230079811-0.0203115074293-0.1385823230760.0297231195501-0.01614130088270.183672416160.0327768861742-0.02121502741410.197938759075-0.02413700589220.158312054904-49.26967276147.97808635921-4.58614031543
96.81165191615.01069674303-1.289661263133.73338882265-1.292330694422.571041284330.111512435398-0.465205714049-0.1377183056520.291615158926-0.166299301493-0.1437905363210.1519356353540.09038345142570.06006984508150.2064530996880.0684825616123-0.001142873246410.218262283279-0.00206820892020.140167185082-48.926880036-4.42110684970.441537762762
101.81026129568-0.03206239250370.02469718670242.039047059030.3037216008823.608965953170.00331699990611-0.15960900467-0.1649325941560.244449188892-0.0603279668450.2875783717160.130722730582-0.2041729517270.04253641058330.1075351355150.01268714089760.03153566892670.145287699468-0.006811543851010.233864954666-83.59138192731.27665500208-31.9895599278
114.63471319148-0.4688620512642.16264699242.336884031681.244245848533.95853729343-0.01542255996810.154383210617-0.2401514168690.00377469185528-0.181952271010.4319183941710.00580120006643-0.3080181158080.2105327901710.132516249805-0.01737315924520.003936380908590.143221660014-0.02404963852210.247408728484-88.22687693752.28600324349-42.9410927871
120.3667777088610.1803514345260.2679827440180.9544677894890.6038762513071.82535534595-0.016154767058-0.02858258524840.00128810920218-0.02531219785080.0173602871110.0129428443964-0.00648317232834-0.0148298278171-0.005939234333850.1209397582980.00701621059344-0.0008925714125620.1447120491650.003008431379440.16067790496-69.58290646086.45712174323-36.1381029598
130.9047759665220.5281136128650.7526476466724.261843816144.096195950915.08961785013-0.08997758697640.1018246916390.0351058013132-0.3863131339190.01365829423510.101877141182-0.286678701317-0.01827432684010.09162421075320.161779996263-0.0012315258708-0.004665659722810.1540462492110.02391571054750.170573287286-70.008208900111.9058071298-48.0932714046
141.08222297693-0.282872385070.4075316040440.660636834523-0.1221908893383.41680337711-0.0895885503379-0.1954835657150.04201278157860.0635311548440.0401071601310.111383576583-0.16919603559-0.3254223664350.0728787945050.1369078485950.03310116467540.007061343991730.129529570632-0.006761547964330.170007632435-76.937472052514.980925055-25.8656608661
151.8186025747-0.2536792427540.3875291600862.83611245222-0.502343537838.1119025289-0.02459423154870.02342077928740.2649236946060.00304542433506-0.009072812284120.0262604307056-0.5075329589920.04892194757650.02172871079760.1389669341240.00461446971928-0.001876736207540.1269652209470.001530865356750.231804976333-74.379806103222.9801974838-34.9404058359
160.781764931273-0.1057214946140.4946519026981.65664883971-1.482010706693.79011093158-0.0896843403461-0.07909335841650.03647221013180.06804180674770.03883485340150.16027099261-0.145992661938-0.1631822087920.02839296144380.1672730187140.02873671385190.004574388982410.176667174938-0.007140349613540.223973696979-84.071369089914.4511117219-30.6761076959
172.68884994086-0.1565515293410.2960835605072.6907688179-2.145563541136.234247210370.0659785995850.1351622565090.0356232468994-0.08273742773320.05156700878310.410515467341-0.0789825785105-0.378590169234-0.1695257782650.1206810893760.0340051410972-0.03218991919180.164483122866-0.02672217903350.292641789681-90.402580199610.771119275-41.4263695513
183.01422187791-0.8078077560730.3049517427683.63889700104-0.2963844228282.384392006320.0496537493664-0.06547173358640.01528573775070.008741282477450.0147413413184-0.269946747998-0.08851703252420.320866064157-0.04907128306460.158266917645-0.05703182555810.03721056849370.210737090079-0.0285731078070.142843345573-36.14990099037.37418692987-58.1395439099
199.37435517138-2.593783905330.1599146827376.265925576911.938586135426.5797066387-0.02476624640110.0931727593170.1049250677410.01297291477830.11611103369-1.11583319819-0.2870808528860.512008411224-0.01636382498940.173437313586-0.09695737463970.01319038690470.26529704641-0.01592112461830.308123427521-26.83008629938.03693829161-56.6411733043
201.52735219144-0.4891183986910.524408523355.13066878296-2.289359369973.978298200050.0960274863010.1580258510520.379565599112-0.404802218554-0.00364078857313-0.404244708299-0.427265280710.513713773108-0.09550087277930.241851339129-0.08405017011430.05937058463290.1989099525060.003557707156290.211534638519-38.368820891615.6035101814-64.6899860328
210.71933087633-0.2496618021790.1493447023321.06979417958-0.05130778380360.7598933101970.002383573703470.05298935193790.0300229042934-0.0956446711234-0.00895704766674-0.0053761159599-0.03749602891040.06385654655390.006143127923770.139567742695-0.01966068182370.0109717307180.171866569678-0.002788174973930.138714773967-46.60246657460.673432710519-55.3573654152
226.83370743625-3.408243940233.995977024793.33948806679-2.348094666774.324214987810.02518585276070.0727763733547-0.358014529515-0.2425666511250.1101834401520.1185962117430.1723701229150.0128640032932-0.1328447292720.191355483244-0.03962857383510.009386185650380.168880546447-0.03026714913360.157242591101-48.469993436-8.61246773832-65.2051049399
234.92846437638-1.555405024081.778739782941.95245648235-0.7685351319682.268444985280.07624922531440.195247790211-0.00704509820864-0.28622628142-0.0206998286568-0.1424823366390.1050908041210.246877115794-0.04111529922060.197088710412-0.02287839126940.0368932063590.197534267247-0.02033608656690.166951930799-36.6664978396-2.03237787858-65.8715822146
247.89461158123-4.446016997282.950947063124.94389379128-1.941794155393.933381907740.1073170759890.5163130667010.439575984766-0.467052878533-0.18054448052-0.354371393214-0.1649013302070.2399123003050.09680186128460.297736869296-0.06400000778780.07279394076020.2298601743360.03382699222930.15176890301-39.21432932149.76302423954-71.2316001031
254.82818284583-1.694747299710.01725095294583.194245818190.07086940999792.20875044776-0.02404762705350.2949398582670.173247585901-0.2223407054930.005470964746520.126254695779-0.12444999809-0.09788693437380.008665203915460.177181474812-0.0534398119839-0.01530405933970.1499085529180.002073479446470.177433028835-45.371818390425.1763666562-49.0867557344
266.82752385827-0.6119813739961.101087516277.342480347020.05911064732425.197642127370.04456665519780.3349400549380.0978144092448-0.429254600448-0.144124035895-0.173789597799-0.270816008495-0.09258160888110.05037193901250.221852760251-0.0499313195383-0.01513208221780.1579679526620.04112424282880.124421450741-48.336191844828.5964457963-55.6909108174
272.58520773757-0.0957467076338-0.6670112113712.63276353189-0.6614664522141.96516216241-0.06073660904520.2330556975850.0160881086645-0.3577351378570.0354471637208-0.11782131487-0.1269799318940.04290115484120.05774300497430.242868675514-0.04575651456930.0223248478070.1877843728020.003685931843510.206076047007-34.341999729725.4816932872-51.9059102256
281.3684377439-0.535541372867-0.6148997337110.7322221793670.4168455611291.02347398953-0.02935463140560.05607871042980.01223676594240.008856272409220.0380371381819-0.0243529517327-0.03311527771080.0330022455467-0.006470272477460.132549980322-0.0144102708378-0.009286020437640.1272478270880.003790408483810.159306639565-47.500472342915.9160596152-39.7806891862
294.09648124791-4.23325790673-4.177411990854.41728305414.234421363154.33468280425-0.169100337901-0.3779251849040.1456388969730.2228118257790.309677809274-0.2273227392520.1813924577960.333611269297-0.1746282816590.142497746871-0.0165249326366-0.01754026695420.199072775256-0.002853164343160.184817044463-40.662720896816.521493847-30.1539584235
304.264373351520.759132280971-2.405672767977.018723612080.6729019475668.73174785269-0.176832964103-0.103655478848-0.445625322816-0.3080270188820.136440313454-1.273502450770.3525753531220.8409634343870.03495215593640.1891306908370.0216449884840.0328236955780.218633016593-0.01732295090060.342495019255-27.93370777788.53199130496-41.3927233565
313.37380188813-0.748675558751-0.04186671689441.00565600738-0.2332048994470.251234522842-0.03978448461620.1268545001840.3449010892-0.007465629491890.02806887427210.0641830107267-0.106004942933-0.0054846305798-0.0005449534725080.188643252901-0.0178640832812-0.02350088331230.132017111359-0.01828576101380.209004285995-52.290092276729.9330644748-36.2698092483
322.9546586508-3.822283419250.7926716017195.3921417154-0.01880589702282.83165488053-0.280762225265-0.3470033928610.2586097466880.3063354583820.145118193581-0.119135988662-0.3862412003480.06695960317210.1464344727370.240129083346-0.0354986177292-0.02008275839130.174093247742-0.02979368259750.173434147554-43.779520520127.5539868365-27.5210670667
337.87554944162-6.152230708852.762373185196.16114760694-2.619013776973.255768895980.0315509475949-0.08203697467770.398715254579-0.0860085645513-0.0108906107883-0.331727207894-0.1658448011230.306176020363-0.0115261761040.183641343965-0.0646485151987-0.01800724474870.20449798172-0.03152341390290.215817998189-35.568813914729.4752954383-34.9296311195
347.30574859425-0.998724956614-0.07577694276290.205169754991-0.2767255286141.09517468032-0.0573576375365-0.2229057577960.413292242038-0.03441105131840.07418276222110.1511234758-0.196543495576-0.0955165647656-0.01302135843890.236734204196-0.00713886461098-0.03140729095210.1694259765150.001899613981210.276540850855-51.027443207635.3623895033-43.0364547006
353.50872056791-2.232949991753.908628432742.98389696035-2.161877833334.4602994056-0.137301448930.3505635950080.0117666388771-0.0122729657617-0.00724186201013-0.111348420593-0.2228921004490.2576811706140.207200043920.194781662385-0.09152187096760.01191935111330.1563958430850.001910142564830.194253998122-33.611082301631.5816885376-45.4356357085
361.96024176071-0.329578135813-0.6691559268151.721524967740.05701885624633.80226573999-0.02532524096290.2242086516170.129835249864-0.157311187033-0.0443375456670.145743887417-0.0795358715583-0.1482002953370.04895814948590.131835586478-0.0351071348971-0.02193534230690.1529362168160.001614846943580.185432197474-77.5987290112-10.2571025117-51.9690787861
376.420208272672.51618424142-2.143678527715.08629637126-0.03292406404355.88979744604-0.0538278018160.151345946340.1670801414220.04892483862960.04995363919580.51637915360.0672868422218-0.3985713025740.03747053448470.1298766640680.0136996512414-0.01299869918540.1297071171660.01178220883320.221924538435-85.3150987395-13.6490147025-43.2690510966
381.26565910574-0.346137248873-0.8679770809870.9307496935920.3673503978341.54466100539-0.008275929263910.02413347940050.006384463504480.05994340753480.005830151272790.009663412851940.0104068789202-0.0186713916214-0.005988619790750.1277661382-0.0089590663546-0.01150743543890.1199956280510.001654606578280.133776306795-65.1049610626-10.1883773523-42.9114538195
394.92562911849-2.91650702427-3.758692963973.342664597663.014140886374.72266009889-0.224977416169-0.193756591228-0.09745443878980.3131606470680.08528464371340.1594121060360.232816413175-0.02000464737020.1900395982110.168996969369-0.004346284010170.005562067625590.1430919128770.01259587937550.153029090925-67.5871173102-16.1764328344-31.4691284839
401.115045052290.208522317584-1.142174631070.420185704347-0.2417260608833.52193310932-0.05286153536190.124121373163-0.0635908740451-0.072419314190.027480474870.03406241364070.153601110762-0.08955201433250.05121651716050.164348511906-0.0122986366285-0.01416324276380.139640866538-0.01662831653480.170253925068-64.7973096949-20.2218378113-54.4427948965
414.267603625161.11096787932-3.641408137173.3291870516-1.406335929553.19955697333-0.176588128347-0.0656228265545-0.387721452775-0.122135535074-0.0092589432587-0.1052799474320.5218509128710.2502854176720.2256412054290.162768782710.00807741630652-0.03051839055470.1232926729360.004903774843010.220799444318-62.4907290182-27.3074410393-44.7573902608
422.0284119983-0.877064565768-1.05995271051.85157420589-1.110140385952.26225665753-0.05188188632430.00549141434522-0.2164489689470.05859683135360.01033678589060.1989863150770.381891695358-0.4084686289540.04411543036270.176616323162-0.02613089248560.0259334453950.1361609241860.007236285782340.227650743111-73.6800713025-26.8863369329-41.9047003697
432.69457440830.956558886016-2.393138144850.986499456212-1.300924030174.43001885865-0.05296324760450.115321709927-0.0879390308322-0.07057865180360.05216264210290.1496494681970.161040696449-0.1818711814280.01534145869310.176399009065-0.0336987418407-0.01736750356850.143616556762-0.01773803690280.218496565364-78.7967478158-21.3462004136-50.5487239962
442.461454675740.7141411914690.2092765575253.204605304140.4236002165562.22011136165-0.0802789970813-0.219519953263-0.1816684280460.3302070856190.09932633948940.09964591393790.230432801146-0.077365566481-0.03141792906090.1602022489040.06887931864920.006469400807640.1459938910810.01620363662980.123642067523-42.9292334169-21.1275169073-19.6887782568
454.74139045150.1338037089452.116441196473.313665504270.8186541250773.45698350564-0.11589246724-0.31264406611-0.1007461524790.5952783692360.182052495216-0.1815335217150.1412395769750.115640718514-0.0513037847330.2084738139290.0607131733926-0.03058782306680.211601588803-0.02050648701570.115032839564-32.9809335311-16.1632942692-14.6775544913
461.019120659860.217957803713-0.0449977472331.245146643610.980464574981.65716262844-0.0289940766515-0.01312340559980.0190513712801-0.03528120581790.0387304468168-0.0281444351418-0.03227633193970.0498594719589-0.004377547325210.1035231769780.00941104031204-0.007525198140730.1113239132570.002438317596980.128772615038-43.7047673726-11.1789459235-31.4738516472
470.5847062639060.4238554509070.7275394985824.336983197213.355671099964.566750724810.02890888792940.02483236072240.05182922741530.05799301751760.21769610537-0.331878907786-0.1457445503220.312101224992-0.3313273168830.133982414151-0.01383902100190.008612464326990.21623356742-0.02398815151370.194717621349-32.5248320849-4.29954096958-32.5368973776
483.214440484451.892104838061.56800936572.443372665970.8251486186480.8544996969470.0834095067574-0.129692458847-0.236716965510.03649820000880.0231360769413-0.08166304719350.1052096188950.0331991099439-0.1329582438190.1653071853640.04029220230070.009433468745760.174241916773-0.01566756997750.18254412453-41.6174276425-25.7723735488-35.4779533156
498.083187090983.824754459951.344017192954.710847865340.7302508315162.14861997053-0.203254611840.28800802701-0.26274831042-0.3759624956170.19128787674-0.3062508961760.07418930429670.290650615391-0.01689539191430.160742123410.04690068287460.0416485746310.207877168118-0.03057589975350.166436319407-32.9130644113-20.551617524-41.1944695671
504.680190800766.0763052424-1.00958665538.41502167023-0.7928724519922.080229575310.04624662266270.128882664531-0.09184063662360.159545085786-0.0154583591709-0.285461099460.09189492042020.44713112892-0.03027297252450.1254514770670.0544079972085-0.006955275373060.289071018345-0.02377006003090.19913761711-26.862988198-19.3601946163-31.0806937199
514.20831058643.536049147481.975430383263.055339578561.476964353681.636816088590.0933106231480.149880429062-0.4406768163440.1431015519740.0752544831884-0.06923526361170.2621999262750.176117802891-0.2065548906010.1855357433060.05177757439880.006942726626780.1562673309690.001394942860960.200447666796-40.8992374174-30.7236105597-28.3735269681
528.824918186387.312448907262.268547745039.354545918751.651083799091.659819033750.0549695293821-0.275046778407-0.3668725330550.4184809573120.087948672095-0.6159543860010.2092054161840.378572446866-0.1103712657620.1762839810540.111456135588-0.02945377987980.28886666757-0.04683319535620.199096044063-27.5515548428-20.8414900134-19.9889647026
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 33 )
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 105 )
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 132 )
6X-RAY DIFFRACTION6chain 'A' and (resid 133 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 176 )
8X-RAY DIFFRACTION8chain 'A' and (resid 177 through 198 )
9X-RAY DIFFRACTION9chain 'A' and (resid 199 through 219 )
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 33 )
11X-RAY DIFFRACTION11chain 'B' and (resid 34 through 51 )
12X-RAY DIFFRACTION12chain 'B' and (resid 52 through 105 )
13X-RAY DIFFRACTION13chain 'B' and (resid 106 through 132 )
14X-RAY DIFFRACTION14chain 'B' and (resid 133 through 155 )
15X-RAY DIFFRACTION15chain 'B' and (resid 156 through 176 )
16X-RAY DIFFRACTION16chain 'B' and (resid 177 through 198 )
17X-RAY DIFFRACTION17chain 'B' and (resid 199 through 219 )
18X-RAY DIFFRACTION18chain 'C' and (resid 0 through 21 )
19X-RAY DIFFRACTION19chain 'C' and (resid 22 through 33 )
20X-RAY DIFFRACTION20chain 'C' and (resid 34 through 51 )
21X-RAY DIFFRACTION21chain 'C' and (resid 52 through 155 )
22X-RAY DIFFRACTION22chain 'C' and (resid 156 through 176 )
23X-RAY DIFFRACTION23chain 'C' and (resid 177 through 198 )
24X-RAY DIFFRACTION24chain 'C' and (resid 199 through 219 )
25X-RAY DIFFRACTION25chain 'D' and (resid 0 through 22 )
26X-RAY DIFFRACTION26chain 'D' and (resid 23 through 33 )
27X-RAY DIFFRACTION27chain 'D' and (resid 34 through 51 )
28X-RAY DIFFRACTION28chain 'D' and (resid 52 through 105 )
29X-RAY DIFFRACTION29chain 'D' and (resid 106 through 122 )
30X-RAY DIFFRACTION30chain 'D' and (resid 123 through 132 )
31X-RAY DIFFRACTION31chain 'D' and (resid 133 through 155 )
32X-RAY DIFFRACTION32chain 'D' and (resid 156 through 176 )
33X-RAY DIFFRACTION33chain 'D' and (resid 177 through 185 )
34X-RAY DIFFRACTION34chain 'D' and (resid 186 through 198 )
35X-RAY DIFFRACTION35chain 'D' and (resid 199 through 219 )
36X-RAY DIFFRACTION36chain 'E' and (resid 0 through 33 )
37X-RAY DIFFRACTION37chain 'E' and (resid 34 through 51 )
38X-RAY DIFFRACTION38chain 'E' and (resid 52 through 105 )
39X-RAY DIFFRACTION39chain 'E' and (resid 106 through 132 )
40X-RAY DIFFRACTION40chain 'E' and (resid 133 through 155 )
41X-RAY DIFFRACTION41chain 'E' and (resid 156 through 176 )
42X-RAY DIFFRACTION42chain 'E' and (resid 177 through 185 )
43X-RAY DIFFRACTION43chain 'E' and (resid 186 through 219 )
44X-RAY DIFFRACTION44chain 'F' and (resid 0 through 33 )
45X-RAY DIFFRACTION45chain 'F' and (resid 34 through 51 )
46X-RAY DIFFRACTION46chain 'F' and (resid 52 through 105 )
47X-RAY DIFFRACTION47chain 'F' and (resid 106 through 132 )
48X-RAY DIFFRACTION48chain 'F' and (resid 133 through 155 )
49X-RAY DIFFRACTION49chain 'F' and (resid 156 through 176 )
50X-RAY DIFFRACTION50chain 'F' and (resid 177 through 185 )
51X-RAY DIFFRACTION51chain 'F' and (resid 186 through 198 )
52X-RAY DIFFRACTION52chain 'F' and (resid 199 through 219 )

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る